# Tags

A tag is a keyword or label that categorizes your question with other, similar questions. Using the right tags makes it easier for others to find and answer your question.

Please supplement your question with a minimal reproducible example. Use dput() for data and specify all non-base packages with library calls. For statistical questions please use http://stats.stackex…
780 questions
if they pertain to issues related to bioinformatics analysis of RNA-seq data, e.g. normalization, differential expression analysis, sequencing and experimental design…
579 questions
python is a programming language, widely used in bioinformatics
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to refer to the alignment of nucleotide or peptide sequences, producing an arrangement that maximizes similarity between sequences.
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for questions related to single-cell RNA-seq.
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To be used for questions specific tothe sequence file format .fasta. Please minimise usage if the question is more generally about sequence formats.
204 questions
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
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The "Binary Alignment Map" (BAM) format is one of the common binary formats used to store sequence alignment information. Questions should include this tag if they directly pertain to the format itsel…
194 questions
These questions are about sequence alignment.
189 questions
Questions relating to proteins, the chains of amino acids that form three-dimensional structures carrying important functions of life. Protein sequence, structure, similarity, domains, etc.
189 questions
VCF, acronym for Variant Calling Format, is a text file type used to store information regarding genetic variants.
183 questions
Biopython is a set of freely available tools for biological computation written in Python.
182 questions
Seurat is a package for analyzing single cell rna seq data.
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Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.
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to refer to the gene sequence/coding part of the sequence.
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for questions related to whole genome analyses. For questions related to individual genes, use tag gene instead. Questions specific to format (like fasta) should be tagged with a format-specific tag.
165 questions
Phylogeny is a statistical approach for reconstructing evolutionary relationships using trees
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The 3-D structure of a protein in space. It can refer to secondary structures, such as alpha helices or beta sheets, or the 3-D coordinates of the atoms making up a protein.
155 questions
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule.
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For statistical questions related to bioinformatics. If the nature of question is purely statistical, consider stats.stackexchange.com instead.
147 questions
Single Nucleotide Polymorphisms. How to find them? How to correlate them with other data? How to represent them? What is their distribution?
141 questions
A repository for data that is organised according to specific rules. Important biological databases include PDB (Protein Data Bank), Ensembl, Uniprot.
139 questions
Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
131 questions
The process of attaching contextual information to a biomolecular (DNA, RNA, or protein) sequence, such as the location of genes, promoters, or repeats in genomic DNA, or the function of a protein.
131 questions
Process of creating the original sequence from the read sequences that it generated during a sequencing experiment. Can refer to genome assembly, in which case the original sequence is a genome, or tr…
127 questions
Umbrella term for understanding any given nucleic acid sequence code, either as a locus, loci or genome with itself or as a comparison to comparable nucleic acid sequence code either intraspecificall…
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Questions about techniques in which the genetic material of a single cell is analysed individually
126 questions
Acronym for deoxyribonucleic acid, the unit of inheritance for all eukaryotic and prokaryotic organisms
117 questions
Deseq2 is an R package for analyzing RNA sequencing data
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Genomics is an interdisciplinary field of science focusing on the structure, function, evolution, mapping, and editing of genomes.
109 questions
Use it when comparing a measure of the expression between two (or more) samples, where the units are relative to the comparison.
109 questions
Basic Local Alignment Search Tool: algorithm that finds regions of similarity between a pair of sequences, can be used to query an unknown sequence against a database of known sequences.
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use for general applications of high-throughput nucleotide sequencing methods that use short-read technology (e.g. Illumina, IonTorrent). For long-read sequencing, use 'long-read', or a more specific …
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A file format used in structural biology to describe the 3-D coordinates of atoms of a biological structure, often a protein. Can also refer to the Protein Data Bank database, which stores all the sub…
105 questions
FASTQ is a file format use to store short reads and their quality values
104 questions